Gene expression profiling in Pekin duck embryonic breast muscle

Transcriptome Profiling Identifies Differentially Expressed Genes in Skeletal Muscle Development in Native Chinese Ducks

China boasts a rich diversity of indigenous duck species, some of which exhibit desirable economic traits. Here, we generated transcriptome sequencing datasets of breast muscle tissue samples from 1D of four groups: Pekin duck pure breeding group (P), Jinling White duck breeding group (J), P ♂ × J ♀ orthogonal group (PJ) and J ♂ × P ♀ reciprocal-cross group (JP) (n = 3), chosen based on the distinctive characteristics of duck muscle development during the embryonic period. We identified 5053 differentially expressed genes (DEGs) among the four groups. Network prediction analysis showed that ribosome and oxidative phosphorylation-related genes were the most enriched, and muscular protein-related genes were found in the 14-day-old embryonic group. We found that previously characterized functional genes, such as FN1, AGRN, ADNAMST3, APOB and FGF9, were potentially involved in muscle development in 14-day-old embryos. Functional enrichment analysis suggested that genes that participated in molecular function and cell component and key signaling pathways (e.g., hippo, ribosome, oxidative phosphorylation) were significantly enriched in the development of skeletal muscle at 14 days of embryonic age. These results indicate a possible role of muscle metabolism and myoglobin synthesis in skeletal muscle development in both duck parents and hybrids.

m6A and miRNA jointly regulate the development of breast muscles in duck embryonic stages

N6-methyladenosine (m6A) is an abundant internal mRNA modification and plays a crucial regulatory role in animal growth and development. In recent years, m6A modification has been found to play a key role in skeletal muscles. However, whether m6A modification contributes to embryonic breast muscle development of Pekin ducks has not been explored. To explore the role of m6A in embryonic breast muscle development of ducks, we performed m6A sequencing and miRNA sequencing for the breast muscle of duck embryos on the 19th (E19) and 27th (E27) days. A total of 12,717 m6A peaks were identified at E19, representing a total of 7,438 gene transcripts. A total of 14,703 m6A peaks were identified, which overlapped with the transcripts of 7,753 genes at E27. Comparing E19 and E27, we identified 2,347 differential m6A peaks, which overlapped with 1,605 m6A-modified genes (MMGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that MMGs were enriched in multiple muscle- or fat-related pathways, which was also revealed from our analysis of differentially expressed genes (DEGs). Conjoint analysis of m6A-seq and RNA-seq data showed that pathways related to β-oxidation of fatty acids and skeletal muscle development were significantly enriched, suggesting that m6A modification is involved in the regulation of fat deposition and skeletal muscle development. There were 90 upregulated and 102 downregulated miRNAs identified between the E19 and E27 stages. Through overlapping analysis of genes shared by MMGs and DEGs and the targets of differentially expressed miRNAs (DEMs), we identified six m6A-mRNA-regulated miRNAs. Finally, we found that m6A modification can regulate fat deposition and skeletal muscle development. In conclusion, our results suggest that m6A modification is a key regulator for embryonic breast muscle development and fat deposition of ducks by affecting expressions of mRNAs and miRNAs. This is the first study to comprehensively characterize the m6A patterns in the duck transcriptome. These data provide a solid basis for future work aimed at determining the potential functional roles of m6A modification in adipose deposition and muscle growth.

Decorin regulates myostatin and enhances proliferation and differentiation of embryonic myoblasts in Leizhou black duck

Skeletal muscle is one of the most important economic traits in the poultry industry whose development goes through several processes influenced by several candidate genes. This study explored the regulatory role of DCN on MSTN and the influence of these genes on the proliferation and differentiation of embryonic myoblasts in Leizhou black ducks. Embryonic myoblasts were transfected with over-expressing DCN, Si-DCN, and empty vector and cultured for 24 h, 48 h, and 72 h of proliferation and the comparative expression of DCN and MSTN were measured. The results showed that cells transfected with the over-expression DCN had a significantly (P < 0.05) higher expression of DCN mRNA than the normal group and the expression of MSTN mRNA showed a downward trend during the proliferation of myoblasts. DCN mRNA expression was lower in cells transfected with Si-DCN than the normal group in all stages of proliferation. While the expression of MSTN in the Si-DCN transfected group was higher than the normal group with a significant (P < 0.05) difference at the 72 h stage. DCN mRNA increased at the early stage of differentiation but decreased (P > 0.05) from the 6th day to the 8th day of differentiation. The level of MSTN increased gradually during the differentiation process of myoblasts until it decreased significantly on the 8th day. These results show that DCN enhances the proliferation and differentiation of Leizhou black duck myoblasts and suppresses MSTN activity.

Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq

In China, the production for duck meat is second only to that of chicken, and the demand for duck meat is also increasing. However, there is still unclear on the internal mechanism of regulating skeletal muscle growth and development in duck. This study aimed to identity candidate genes related to growth of duck skeletal muscle and explore the potential regulatory mechanism. RNA-seq technology was used to compare the transcriptome of skeletal muscles in black Muscovy ducks at different developmental stages (day 17, 21, 27, 31, and 34 of embryos and postnatal 6-month-olds). The SNPs and InDels of black Muscovy ducks at different growth stages were mainly in “INTRON”, “SYNONYMOUS_CODING”, “UTR_3_PRIME”, and “DOWNSTREAM”. The average number of AS in each sample was 37,267, mainly concentrated in TSS and TTS. Besides, a total of 19 to 5377 DEGs were detected in each pairwise comparison. Functional analysis showed that the DEGs were mainly involved in the processes of cell growth, muscle development, and cellular activities (junction, migration, assembly, differentiation, and proliferation). Many of DEGs were well known to be related to growth of skeletal muscle in black Muscovy duck, such as MyoG, FBXO1, MEF2A, and FoxN2. KEGG pathway analysis identified that the DEGs were significantly enriched in the pathways related to the focal adhesion, MAPK signaling pathway and regulation of the actin cytoskeleton. Some DEGs assigned to these pathways were potential candidate genes inducing the difference in muscle growth among the developmental stages, such as FAF1, RGS8, GRB10, SMYD3, and TNNI2. Our study identified several genes and pathways that may participate in the regulation of skeletal muscle growth in black Muscovy duck. These results should serve as an important resource revealing the molecular basis of muscle growth and development in duck.

Characterization of microRNAs during Embryonic Skeletal Muscle Development in the Shan Ma Duck

Simple Summary

It is of great commercial interest to elucidate the genetic mechanisms associated with skeletal muscle development in the duck. In this study, we performed high throughput microRNA (miRNA) sequencing to identify the candidate miRNAs during two developmental stages of duck embryonic breast muscle. We detected 1091 miRNAs and 109 of them were differentially expressed between embryonic day 13 (E13) and E19. We also predicted the target genes of the differentially expressed miRNAs and subsequently analyzed the enriched gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways, and finally constructed a protein–protein interaction (PPI) network with the target genes. Luciferase reporter assay showed that the growth-related genes, Fibroblast growth factor receptor like 1 (FGFRL1) and Insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1), were target genes of miR-214-5p. These results can supplement the duck miRNA database and provide several candidate miRNAs for future studies on the regulation of embryonic skeletal muscle development.

Abstract

Poultry skeletal muscle provides high quality protein for humans. Study of the genetic mechanisms during duck skeletal muscle development contribute to future duck breeding and meat production. In the current study, three breast muscle samples from Shan Ma ducks at embryonic day 13 (E13) and E19 were collected, respectively. We detected microRNA (miRNA) expression using high throughput sequencing following bioinformatic analysis. qRT-PCR validated the reliability of sequencing results. We also identified target prediction results using the luciferase reporter assay. A total of 812 known miRNAs and 279 novel miRNAs were detected in six samples; as a result, 61 up-regulated and 48 down-regulated differentially expressed miRNAs were identified between E13 and E19 (|log2 fold change| ≥ 1 and p ≤ 0.05). Enrichment analysis showed that target genes of the differentially expressed miRNAs were enriched on many muscle development-related gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially mitogen-activated protein kinase (MAPK) signaling pathways. An interaction network was constructed using the target genes of the differentially expressed miRNAs. These results complement the current duck miRNA database and offer several miRNA candidates for future studies of skeletal muscle development in the duck.

Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos

Duck (Anas platyrhynchos), one of the most economically important waterfowl, is an ideal model for studying the immune protection mechanism of birds. An incomplete duck reference genome and very limited availability of full-length cDNAs has hindered the identification of alternatively spliced transcripts and slowed down many basic studies in ducks. We applied PacBio Iso-Seq technologies to multiple tissues from duck for use in transcriptome sequencing. We obtained 199,993 full-length transcripts and comprehensively annotated these transcripts. 23,755 lncRNAs were predicted from all identified transcripts and 35,031 alternative splicing events, which divided into 5 models, were accurately predicted from 3,346 genes. Our data constitute a large increase in the known number of both lncRNA, and alternatively spliced transcripts of duck and plays an important role in improving current genome annotation. In addition, the data will be extremely useful for functional studies in other birds.

Mechanism and Functions of Identified miRNAs in Poultry Skeletal Muscle Development – A Review

Development of the skeletal muscle goes through several complex processes regulated by numerous genetic factors. Although much efforts have been made to understand the mechanisms involved in increased muscle yield, little work is done about the miRNAs and candidate genes that are involved in the skeletal muscle development in poultry. Comprehensive research of candidate genes and single nucleotide related to poultry muscle growth is yet to be experimentally unraveled. However, over a few periods, studies in miRNA have disclosed that they actively participate in muscle formation, differentiation, and determination in poultry. Specifically, miR-1, miR-133, and miR-206 influence tissue development, and they are highly expressed in the skeletal muscles. Candidate genes such as CEBPB, MUSTN1, MSTN, IGF1, FOXO3, mTOR, and NFKB1, have also been identified to express in the poultry skeletal muscles development. However, further researches, analysis, and comprehensive studies should be made on the various miRNAs and gene regulatory factors that influence the skeletal muscle development in poultry. The objective of this review is to summarize recent knowledge in miRNAs and their mode of action as well as transcription and candidate genes identified to regulate poultry skeletal muscle development.

Effects of force-feeding on immunology, digestive function and oxidative stress in the duodenal and jejunal mucosa of Pekin ducks

Force-feeding was considered as a traditional high-efficiency approach to improve growth performance and accelerate fat deposition of Pekin ducks. However, force-feeding is a serious violation of international advocacy on animal welfare, because it can induce serious injuries to animals, such as damages to the digestive tract, effects on immunity and even severe oxidative stress. Therefore, it is urgent to stop force-feeding. The aim of this study was to determine the effects of force feeding on immune function, digestive function and oxidative stress in the mucosa of duodenum and jejunum of Pekin ducks. A total of 500 ducks were randomly divided into two groups. The control group was allowed to feed freely on a basal diet. The experimental group was force-fed by inserting a plastic feeding tube 8 to 10 inches long down the esophagus for 6 days. Compared with the control group, there was a significant (P<0.05) increase in serum diamine oxidase, d-lactic acid, endotoxin and corticosterone levels in the force-feeding group. The crypt depth in duodenum and jejunum showed significant differences (P<0.05) between the two groups and the intestinal villus epithelium cell was severely damaged in force-feeding group. Similarly, the activities of digestive enzymes as well as the levels of immune function in the duodenal and jejunal mucosa in the force-feeding group were significantly higher than the control group (P<0.05). However, there was a significant decrease in the superoxide dismutase, glutathione peroxidase and catalase levels with a marked increase in malondialdehyde level in duodenal and jejunal mucosa (P<0.05). In summary, at the end of the fattening period with force-feeding for 6 days, Pekin ducks experienced an adverse effect on the integrity of their duodenal and jejunal mucosa epithelium cell as well as their immune function and antioxidant capacity of Pekin ducks but also had improvement in digestive enzyme activities.

Analysis of Anasplatyrhynchos genome resequencing data reveals genetic signatures of artificial selection

Three artificially selected duck populations (AS), higher lean meat ratios (LTPD), higher fat ratios (FTPD) and higher quality meat (CMD), have been developed in China, providing excellent populations for investigation of artificial selection effects. However, the genetic signatures of artificial selection are unclear. In this study, we sequenced the genome sequences of these three artificially selected populations and their ancestral population (mallard, M). We then compared the genome sequences between AS and M and between LTPD and FTPD using integrated strategies such as anchoring scaffolds to pseudo-chromosomes, mutation detection, selective screening, GO analysis, qRT-PCR, and protein multiple sequences alignment to uncover genetic signatures of selection. We anchored duck scaffolds to pseudo-chromosomes and obtained 28 pseudo-chromosomes, accounting for 84% of duck genome in length. Totally 78 and 99 genes were found to be under selection between AS and M and between LTPD and FTPD. Genes under selection between AS and M mainly involved in pigmentation and heart rates, while genes under selection between LTPD and FTPD involved in muscle development and fat deposition. A heart rate regulator (HCN1), the strongest selected gene between AS and M, harbored a GC deletion in AS and displayed higher mRNA expression level in M than in AS. IGF2R, a regulator of skeletal muscle mass, was found to be under selection between FTPD and LTPD. We also found two nonsynonymous substitutions in IGF2R, which might lead to higher IGF2R mRNA expression level in FTPD than LTPD, indicating the two nonsynonymous substitutions might play a key role for the regulation of duck skeletal muscle mass. Taken together, these results of this study provide valuable insight for the genetic basis of duck artificial selection.